The abbot named Phra Dhammajayo is accused of money laundering and embezzling funds from the influential temple.
Dhammajayo, 72, has stayed inside the temple for months due to poor health. It is seen as an attempt by the abbot to avoid questioning.
But the abbot and his followers have denied the allegations, claiming they are politically motivated.
Several devotees gathered outside the sprawling temple complex, making it tough for the police to enter the complex.
The devotees of the temple released a statement saying Phra Dhammajayo was severely ill and would only enter the judicial process when the country returns to democracy. Thailand is under military rule since it took over in a coup in 2014.
The temple was founded in the 1970s and it is different from other temples of the Thailand because it has more of the character of a charismatic cult. The temple offers tightly choreographed mass meditations at its bizarre, flying saucer-like central chedi.
Police arrived at the temple at 09:00 local time (02:00 GMT), but the monks did not allow them to enter the premises. Police Maj Suriya Singhakamol, deputy director-general of the Department of Special Investigations (DSI), said unarmed officers eventually "went inside the temple to negotiate".
"Today's operation must be carried out in an orderly manner, nobody should be injured, and everything should be done according to the law," he told reporters.